Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
0
votes
0
replies
618
views
News:
BioC2024 in-person registration closes soon (July 10)
BioC2024
Conference
Bioconductor
Community
17 months ago
Maria Doyle
▴ 110
0
votes
1
reply
641
views
unreal negative log2fc values
DESeq2
des
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
Atul K.
• 0
0
votes
0
replies
426
views
Error in bam loading in getUniqueCleavageEvents() in GUIDEseq package
GUIDEseq
17 months ago
StayM
• 0
0
votes
0
replies
1.6k
views
Job:
Toxicogenomics Statistician
JobPosting
updated 17 months ago by
shepherl
4.2k • written 21.6 years ago by
Warnes, Gregory R
▴ 460
0
votes
0
replies
41
views
Spam:
GenOMICC DNA biobank
alabaster.schemas
db0
17 months ago
Jolka
0
0
votes
1
reply
686
views
Create a Graph w/ Only the Genes Interaction
EnrichedPathways
GeneInteractionGraph
graph
17 months ago
Antonio
• 0
0
votes
0
replies
505
views
EPIC v2 annotation and BigWig
EPICv2manifest
IlluminaHumanMethylationEPICv2anno.20a1.hg38
17 months ago
MajaVu
• 0
0
votes
1
reply
558
views
LRT test for different timepoints (one tissue types vs. many tissue types)
DESeq2
updated 17 months ago by
Michael Love
43k • written 17 months ago by
K
• 0
0
votes
0
replies
731
views
Improving Gene Matching for CIBERSORT Deconvolution with Monaco Reference Matrix in Bulk RNA-Seq
DeconRNASeq
AnnotationDbi
org.Hs.eg.db
17 months ago
chunglee13
• 0
0
votes
4
replies
1.8k
views
Trouble Installing DADA2 (warning: R new user)
dada2
updated 17 months ago by
shepherl
4.2k • written 17 months ago by
schott01
• 0
0
votes
0
replies
721
views
Difference in Predictive component of PLS and OPLS Model
Metabolomics
plotGrouper
Bioconductor
ropls
PLSDAbatch
17 months ago
devarti.mahakalkar
• 0
0
votes
0
replies
720
views
Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
minfi
EPICv2manifest
MethylAid
17 months ago
pcibin
• 0
0
votes
4
replies
9.0k
views
Any tools to convert .gff to .gtf format
AnnotationData
CrispRdesignR
BSgenome
updated 11 months ago by
ControlF5
• 0 • written 3.3 years ago by
Manoj Kumar R
• 0
0
votes
3
replies
963
views
Conumee with EPICv2 Segment function
Conu
conumee
updated 8 months ago by
zpingfeng
• 0 • written 17 months ago by
idatta1
• 0
0
votes
0
replies
854
views
Job:
Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
Bioinformatics
scRNAseq
17 months ago
Damini
• 0
0
votes
1
reply
693
views
single excel file containing methylation beta values does not get loaded in ChAMP
ChAMP
updated 17 months ago by
Basti
▴ 780 • written 17 months ago by
tahirah.yasmin2014
• 0
1
vote
2
replies
775
views
How to get the DMR?
ENmix
17 months ago
Alex
• 0
0
votes
0
replies
389
views
Remove Control Probes from Affymetrix Human Gene 1.0 ST Array probeset version
AffymetrixDataTestFiles
AffymetrixChip
17 months ago
drexjaramel
• 0
0
votes
3
replies
993
views
How to search Pubmed Central or other fulltext literature base using regex?
metaMSdata
Bioconductor
17 months ago
Abiologist
• 0
0
votes
1
reply
3.4k
views
converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5
SingleCellExperiment
BPCells
SingleCellExper
updated 17 months ago by
yxsee
• 0 • written 17 months ago by
Le
• 0
0
votes
0
replies
499
views
Understanding Differentially Abundant Neighbourhood Identification
miloR
17 months ago
Dario Strbenac
★ 1.6k
2
votes
2
replies
5.6k
views
Unable to install the package "tissuesGeneExpression"
bioconductor
updated 17 months ago by
Muhammad Abdullah
• 0 • written 8.4 years ago by
mdroog
▴ 10
1
vote
13
replies
2.4k
views
Ranking the GSEA Results
fgsea
log2FC
17 months ago • updated 16 months ago
V_Vibes
• 0
1
vote
8
replies
1.9k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2
glmGamPoi
offset
edgeR
scRNAseq
updated 17 months ago by
Gordon Smyth
53k • written 17 months ago by
Alec
• 0
0
votes
2
replies
1.2k
views
Species level information couldn't find with DADA2 bioconductor package
Metagenomics
dada2
MicrobiomeData
17 months ago • updated 15 months ago
abhisek001
• 0
3
votes
1
reply
2.1k
views
Difference between enrichGO results and Enrichr website results
Pathways
GO.db
clusterProfiler
updated 17 months ago by
Guido Hooiveld
★ 4.1k • written 17 months ago by
adrip
▴ 10
0
votes
1
reply
561
views
Risa package missing from Bioconductor 3.19
3.19
Risa
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
rkjulian
• 0
1
vote
2
replies
1.2k
views
Struggling to convert a large list of non-model genes into human orthologs, any suggestions?
annotation
17 months ago
ronin
• 0
0
votes
0
replies
715
views
Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution
rnaseqGene
RNAseq
17 months ago
JG13
• 0
0
votes
1
reply
742
views
BiomaRt listAttributes - which are external ?
Bioconductor
getBM
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
Abiologist
• 0
0
votes
0
replies
810
views
Blacklist regions on DBA object (diffbind)
DiffBind
chipseq
17 months ago
gamma.jian
▴ 10
1
vote
2
replies
3.2k
views
Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment.
DESeq2
17 months ago
sropri
• 0
0
votes
5
replies
1.1k
views
modelGeneVarByPoisson error selecting bandwidth automatically
scran
updated 17 months ago by
Peter Hickey
▴ 760 • written 17 months ago by
Lluís Revilla Sancho
▴ 760
1
vote
4
replies
2.4k
views
SeSAMe DMR for EPIC V2
sesame
EPICv2manifest
epicv2
updated 4 months ago by
MargaretJDinan
• 0 • written 17 months ago by
luca.s
▴ 50
1
vote
5
replies
2.1k
views
EnsDb: bad_weak_ptr
AnnotationHub
BiocFileCache
17 months ago
Lluís Revilla Sancho
▴ 760
0
votes
5
replies
2.1k
views
Cannot connect to annotationhub server
AnnotationHub
ExperimentHub
updated 17 months ago by
shepherl
4.2k • written 17 months ago by
Mishaal Irfan
• 0
4
votes
4
replies
1.7k
views
Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
limma
adjustment
voom
removeBatchEffect
covariates
17 months ago
sukeshinik5
▴ 20
0
votes
0
replies
469
views
Structural Variant Format Converted for BRASS Format
StructuralVariantAnnotation
17 months ago
Dario Strbenac
★ 1.6k
0
votes
1
reply
569
views
Deseq2 design matrix
DESeq2
Designmatrix
limma
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
Neha
• 0
1
vote
2
replies
1.5k
views
Issues with retrieving mouse SNP dataset: biomaRt error: looks like we're connecting to incompatible version of BioMart.
biomaRt
17 months ago
Svitlana
▴ 10
0
votes
0
replies
472
views
Differential Gene Wrapper for Propotion of Detected
scran
17 months ago
Dario Strbenac
★ 1.6k
0
votes
2
replies
1.7k
views
PCA (Principal Component Analysis) plots from ChIP-seq data
ChIPseqR
17 months ago
egbastakis
• 0
4
votes
4
replies
1.1k
views
Warning message when running limma with covariates
limma
17 months ago • updated 11 months ago
Chris
▴ 20
0
votes
9
replies
1.5k
views
Research Project - Expanding search funtionality on the GEO database
GEOquery
GEO
17 months ago
gallantk5
• 0
3
votes
5
replies
3.3k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 17 months ago by
Reza Ghamsari
• 0 • written 21 months ago by
Jack S.
▴ 60
0
votes
8
replies
2.2k
views
limma comparison for small sample size and how to get covariance matrix
covariancematrix
limma
17 months ago
jiachengd
• 0
5
votes
5
replies
1.7k
views
Limma with covariates
limma
written 17 months ago by
Chris
▴ 20
1
vote
1
reply
773
views
DESeq2 - vst() - log2FC - no replicates
DESeq2
log2FC
vst()
updated 17 months ago by
ATpoint
★ 5.0k • written 17 months ago by
lifeonmars
• 0
0
votes
2
replies
1.2k
views
Epicv2 conversion fail
minfi
17 months ago
Alex
• 0
1
vote
5
replies
1.1k
views
DESeq2 ML Query
DESeq2
updated 16 months ago by
Michael Love
43k • written 17 months ago by
chris2.a.white
• 0
46,691 results • Page
20 of 934
Recent ...
Replies
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR
by
efoss
▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma
by
Gordon Smyth
53k
Answered here: https://support.bioconductor.org/p/16318/
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards
• All
Commentator
to
sina.nassiri
▴ 130
Popular Question
to
Hervé Pagès
16k
Popular Question
to
jared.andrews07
▴ 30
Popular Question
to
James W. MacDonald
68k
Popular Question
to
shepherl
4.2k
Locations
• All
Austria,
5 minutes ago
The city by the bay,
41 minutes ago
Germany,
44 minutes ago
WEHI, Melbourne, Australia,
51 minutes ago
University of Eastern Finland,
1 hour ago
Traffic: 680 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6